If you take the leveled height, minus the GPS derived ellipsoid height, how does the difference compare to the geoid separations for the points? It should be close. If they compare very closely you can probably get away with computing an average value that will take you from ellipsoid heights to leveled heights. For the site you could take an average of the difference between ellipsoid heights and leveled heights and input that into the elevation field in the transformation settings screen. Just make sure you set the vertical datum to ellipsoid.

Option 2

The other thing you can do is setup the control points in FieldGenius so that you have the leveled heights defined for them, and set the vertical datum to a geoid, such as NAVD88. Tie in the control points with GPS and on the control page for each point turn off the "hold horizontal", and leave on the "hold vertical" toggles. This will solve for only the vertical positions and will end up computing an elevation difference between the geoid, and your leveled heights. The good thing about doing this is you will be able to see the delta difference in the heights at each point in the transformation settings screen.

With option 2, you can also experiment with using the "Do not calculate vertical slopes" checkbox on the Edit Control page. If this is on then FieldGenius will not tilt the plane to best fit the control points. Sometimes tilting the plane can give you better results which can be confirmed by observing the elevation deltas.

Mike, not sure what the separation is, but another thought - can you create a model (surface) of the separation differences, another model (surface) of the Levelled levels. Then you can take the 1st from the 2nd.
I realise its a bit involved but not really sure what you'r trying to achieve.
Once the Geoid model is set up then thats it - no more messing about.
I assume you are working to fairly fine tolerances over the area and the Levelled 'levels' are up to those standards?
I'm not sure if you are looking at RTK stuff or post process the actual results.
regards
Richard